Ontology highlight
ABSTRACT:
PROVIDER: PRJNA390768 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5693411_1.fastq.gz | Fastqsanger.gz | |||
| SRR5693411_2.fastq.gz | Fastqsanger.gz | |||
| SRR5693412_1.fastq.gz | Fastqsanger.gz | |||
| SRR5693412_2.fastq.gz | Fastqsanger.gz | |||
| SRR5693413_1.fastq.gz | Fastqsanger.gz |
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Project description:The potato cyst nematodes (PCN), Globodera pallida and Globodera rostochiensis, are important parasites of potato. PCN have complex, biotrophic interactions with their hosts that involve gene expression changes in both the nematode and the host plant. The aim of this study is to determine key genes that are differentially expressed in Globodera pallida life cycle stages and during the initiation of the feeding site in susceptible or partially resistant potato genotypes. For this purpose, two microarray experiments were designed: i) a comparison of eggs, infective second stage juveniles (J2) and sedentary parasitic stage J2s (SJ2); ii) a comparison of SJ2 at eight days after inoculation (DAI) in the susceptible cultivar (Desiree) and two partially resistant lines. The data set in this submission came from experiment (I). The results show differential expression of G. pallida genes during the stages studied, including previously characterized effectors. Also, a large number of genes changed their expression between the SJ2 in the susceptible cultivar compared to those infecting partially resistant lines; the number of genes with modified expression were smaller when two partially resistant lines were compared. Additionally, a histopathological study was performed at several time points (7, 14 and 30 DAI) showing the similarities between both partially resistant lines with a delay and degeneration in the formation of the syncytia in comparison to the susceptible cultivar. Females at 30 DAI in partially resistant lines showed a delay in their development in comparison to the susceptible cultivar.
2012-04-12 | E-MTAB-999 | biostudies-arrayexpress
Project description:The potato cyst nematodes (PCN), Globodera pallida and Globodera rostochiensis, are important parasites of potato. PCN have complex, biotrophic interactions with their hosts that involve gene expression changes in both the nematode and the host plant. The aim of this study is to determine key genes that are differentially expressed in Globodera pallida life cycle stages and during the initiation of the feeding site in susceptible or partially resistant potato genotypes. For this purpose, two microarray experiments were designed: i) a comparison of eggs, infective second stage juveniles (J2) and sedentary parasitic stage J2s (SJ2); ii) a comparison of SJ2 at eight days after inoculation (DAI) in the susceptible cultivar (Desiree) and two partially resistant lines. The data set in this submission came from experiment (ii). (Experiment (I) has also been deposited in ArrayExpress under accession E-MTAB-999). The results show differential expression of G. pallida genes during the stages studied, including previously characterized effectors. Also, a large number of genes changed their expression between the SJ2 in the susceptible cultivar compared to those infecting partially resistant lines; the number of genes with modified expression were smaller when two partially resistant lines were compared. Additionally, a histopathological study was performed at several time points (7, 14 and 30 DAI) showing the similarities between both partially resistant lines with a delay and degeneration in the formation of the syncytia in comparison to the susceptible cultivar. Females at 30 DAI in partially resistant lines showed a delay in their development in comparison to the susceptible cultivar.
2012-04-12 | E-MTAB-1010 | biostudies-arrayexpress
Project description:DNA sequencing of nine Globodera pallida populations selected either for four generations on the resistant potato variety Seresta (S4), or, as a control, for one generation on the susceptible variety Desiree (D). Seresta contains GpaV from Solanum vernei as a major resistance against G. pallida. These nine populations were obtained from Dutch potato fields, where they previous to the further selection already showed some degree of virulence on resistant potato varieties. The goal of the experiment was to identify polymorphic loci in the genome associated with the selection on Seresta.
2026-03-16 | E-MTAB-16285 | biostudies-arrayexpress
Project description:We aimed to identify loci under selection for virulence in the potato cyst nematode Globodera pallida. Therefore, two G. pallida populations with suspected virulence, designated AMPOP02 and AMPOP10, were used in a selection experiment on the resistant potato variety Seresta. The selection experiment started in 2015, going through one generation per year, leading to fourth-generation selection populations at the end of 2018. The experiment was conducted in large pots, with a population that was as large as possible. After each generation cysts were saved for a later pot-experiment. This pot experiment was conducted in 2019 where the replication of these G. pallida populations on a set of potato cultivars (amongst others the non-resistant cultivar Desiree and the resistant cultivar Seresta). The first priority with the resulting generation was quantification and thereafter the material resulting from the Desiree and Seresta propagation was frozen in liquid nitrogen for DNA isolation. For each generation/potato cultivar combination three replicates were conducted. In total we had therefore 60 samples. Unfortunately, after DNA isolation, we had material of sufficient quantity and quality to conduct DNA sequencing on 45 samples.
2025-08-05 | E-MTAB-15408 | biostudies-arrayexpress
Project description:We explored the sex determination of Globodera pallida. To do so, we grew cuttings of the potato cultivar Desiree on Gamborg B5 medium supplemented with either 1.5 g/L or 20 g/L sucrose. 14-day-old cuttings were inoculated with 100 G. pallida E400 Rookmaker juveniles. Infected root tissue was harvested at 1, 3, 6, and 9 dpi. Also, a subsample of the ppJ2 was kept for each batch. The experiment contains four time-separated batches. Small RNA sequencing was performed by BGI Hong Kong.
2025-11-05 | E-MTAB-15069 | biostudies-arrayexpress
Project description:We explored the sex determination of Globodera pallida. To do so, we grew cuttings of the potato cultivar Desiree on Gamborg B5 medium supplemented with either 1.5 g/L or 20 g/L sucrose. 14-day-old cuttings were inoculated with 100 G. pallida E400 Rookmaker juveniles. Infected root tissue was harvested at 1, 3, 6, and 9 dpi. Also, a subsample of the ppJ2 was kept for each batch. The experiment contains four time-separated batches. Transcriptome sequencing was performed by BGI Hong Kong. Two samples (B_4.2_1,5; B_4.3_1,5) were not taken along for sequencing because of a failed library prep.
2025-11-25 | E-MTAB-16117 | biostudies-arrayexpress
Project description:The potato powdery scab agent Spongospora subterranea causes damage on the skin of tubers and induces root gall formation, precipitating considerable yield and quality losses. Currently, there are no effective chemical treatments for the control of powdery scabs. Understanding the inducible defence responses in roots of potato plants in the resistant and susceptible host environment, particularly during colonisation of the root by S. subterranea is required for the breeding of novel resistant cultivars. Here, we integrated transcriptomics, proteomics and metabolomics datasets to uncover the mechanisms underlying of the potato resistance to powdery scab. This multi-omics approach identified upregulation of glutathione metabolism at the levels of RNA, protein and metabolite in the resistant cultivar but not in the susceptible cultivar. Upregulation of the lignin metabolic process was also specific to in the resistant cultivar at the transcriptome level. In addition, Tthe inositol phosphate pathway was differentially expressed between two cultivars in response to S. subterranea infection, where it was upregulated in the susceptible cultivar but downregulated in the resistant cultivar. We provide, for the first time, large-scale multi-omics data of Spongospora-potato interaction, thereby suggesting the signaling role of glutathione metabolism in the potato resistance against powdery scab
2022-08-12 | PXD029381 | Pride
Project description:Potato is one of the most important food crops for human consumption. The obligate biotrophic pathogen Spongospora subterranea infects potato roots and tubers, resulting in considerable loss of potato tuber yield and quality. A comprehensive understanding of how potato plants respond to S. subterranea infection is essential for the development of pathogen-resistant crops. Here we employed label-free proteomics and phosphoproteomics to quantify protein-level responses of the susceptible and resistant potato cultivars in response to S. subterranea. A total of 2669 proteins and 1498 phosphoproteins were quantified in the leaf samples of the different treatment groups. Following statistical analysis of the proteomic data, oxidoreductase activity, electron transfer, and photosynthesis were identified as significant processes that differentially changed upon infection specifically in the resistant cultivar and not in the susceptible cultivar. The phosphoproteomics results indicated increased activity of signal transduction and defence response functions in the resistant cultivar. In contrast, the majority of increased phosphoproteins in the susceptible cultivar were related to transporter activity and localisation. This study provides new insight into the molecular mechanisms involved in potato resistance to S. subterranea infection and has highlighted the critical roles of protein phosphorylation in the regulation of potato immune response.
2022-04-07 | PXD031529 | Pride
Project description:In this experiment we follow the infection of potato by Globodera pallida populations AMPOP02 and Rookmaker. The goal of the experiment was twofold: (i) to follow the expression of effectors in the nematode, (ii) to follow the transcriptional response of the potato plant. In this experiment, we inoculated 14 day old potato cuttings of the variety Seresta with AMPOP02, Rookmaker, or a mock-infection. Root tissue was harvested at 1, 3, 6 and 9 days post infection. Also, a subsample of the pre-parasitic juveniles used as the inoculum was kept for each batch. The experiment contains four time-separated batches. RNA extraction was done in Wageningen. Sequencing was performed by BGI Hong Kong.
2025-08-05 | E-MTAB-15312 | biostudies-arrayexpress
Project description:For potato crops, host resistance is currently the most effective and sustainable tool to manage potato root and tuber diseases caused by the plasmodiophorid, Spongospora subterranea. Arguably, zoospore root attachment is the most critical phase of the pathogen infection, however, the mechanisms underlying zoospore root attachment remains unknown. This study investigated the potential role of root cell wall surface polysaccharides and proteins in zoospore root attachment in resistant and susceptible potato cultivars. We first compared the effects of enzymatic removal of root cell wall proteins, N-linked glycans or polysaccharides on S. subterranea attachment to root tissue of resistant and susceptible potato cultivars. Subsequently, mass spectrometry analysis of peptides released by trypsin shaving (TS) of root segments identified 1235 proteins, of which 262 were differentially abundant between the resistant and susceptible cultivars. In particular, proteins associated with glutathione metabolism and lignin biosynthesis were more abundant in the resistant cultivar. Comparison with whole-root proteomic analysis of the same resistant and susceptible cultivars led to identification of 226 proteins unique to the TS dataset, of which 188 were significantly different between cultivars. Among these, the pathogen defence-related cell wall protein stem 28 kDa glycoprotein and two major latex proteins were significantly less abundant in the resistant cultivar compared to the susceptible cultivar. A further major latex protein was detected at reduced levels in the resistant cultivar in both TS and whole-root proteomic datasets. In contrast, in the TS-specific dataset, three glutathione S-transferase proteins were more abundant in the resistant cultivar, while the protein glucan endo-1,3-beta-glucosidase was significantly increased in both the TS and whole-root datasets. These results imply a particular role of major latex proteins and glucan endo-1,3-beta-glucosidase in the regulation of host susceptibility to S. subterranea.
2023-03-11 | PXD037060 | Pride